重要食药同源植物余甘子转录组微卫星特征分析

doi:10.7525/j.issn.1673-5102.2019.02.016

摘要/Abstract

摘要： 为全面了解余甘子转录组SSR位点的分布特征和变异规律，本研究利用Illumina Hiseq 4000平台对余甘子叶片转录组进行测序，通过MISA软件对获得的Unigenes进行SSR位点搜索和统计分析。结果发现9 538条包含SSR位点的Unigenes，共检测到9 991个SSR位点，平均每5.49 kB出现1个SSR。单碱基和二碱基为余甘子转录组SSR主要重复类型，分别占SSR总数的42.3%和30.79%。位于基因编码区的SSR位点共有1 731个，出现频率为0.039 SSRs/kB，优势重复类型为三碱基重复。余甘子转录组SSR中共有169种重复基元，其中所占比例最高的是A/T（42.10%），其次是AG/CT（22.91%）和AAG/CTT（5.02%）。SSR各基元的重复次数波动于4~75次，且多数集中于4~20次。重复片段长度≥ 20 bp的SSR占21.20%，且SSR发生频率与片段长度呈显著负相关（P<0.01），相关系数为-0.561。本研究获得的余甘子转录组SSR位点出现频率较高、分布密度较大、低级重复基元较多，重复次数较高、长片段较多，大多数SSR位点的多态性潜能较高，用于余甘子遗传多样性分析的潜力较大，为下一步余甘子转录组SSR标记的大规模开发和群体遗传学研究提供了重要的数据信息，进而为余甘子野生资源的保护和合理开发利用提供了参考依据。

关键词: 余甘子, 食药同源植物, 转录组测序, 微卫星

Abstract: In order to comprehensively understand the characteristics of distribution and variation of the SSR loci in the transcriptome of Phyllanthus emblica L., transcriptome sequencing was conducted on young leaves of P.emblica by using Illumina Hiseq 4000. The SSR loci were studied using MISA software from the obtained unigenes. A total of 9 991 SSRs distributed on 9 538 unigenes were detected, with an average density of one SSR per 5.49 kB. Mononucleotide and dinucleotide repeats were the main SSR types, accounting for 42.3% and 30.79% of all SSRs, respectively. There were 1 731 SSR loci distributed across the protein-coding regions, with an overall density of 0.039 SSRs/kB. The dominant repeat type was trinucleotide repeat type. Among all the 169 repeat motifs, A/T(42.10%) was the richest motif, followed in order by AG/CT(22.91%) and AAG/CTT(5.02%). The number of repeats ranged from 4 to 75, most of them were concentrated on four to 20. The SSRs with repeat fragment length ≥20 bp accounted for 21.20%. There was significant negative correlation(P<0.01) between the frequency of SSRs and the repeat fragment length, with correlation coefficient of -0.561. The SSR loci in the transcriptome of P.emblica showed high frequency and density of distribution, rich low-level repeat motifs, large repeat number and long fragments, most of which exhibited high potential of polymorphisms in our study. These SSR loci would lay an important foundation for further developing a large number of EST-SSRs and studying on population genetics of P.emblica, and they would also provide a reference for conservation and rational exploitation of genetic resources of the species.

Key words: Phyllanthus emblica, edible and medicinal plant, transcriptome sequencing, microsatellite

中图分类号:

S722

刘雄芳, 李太强, 张序, 李正红, 万友名, 安静, 刘秀贤, 马宏. 重要食药同源植物余甘子转录组微卫星特征分析[J]. 植物研究, 2019, 39(2): 294-302.

LIU Xiong-Fang, LI Tai-Qiang, ZHANG Xu, LI Zheng-Hong, WAN You-Ming, AN Jing, LIU Xiu-Xian, MA Hong. Characteristic Analysis of Microsatellites in the Transcriptome of Phyllanthus emblica,an Important Edible and Medicinal Plant[J]. Bulletin of Botanical Research, 2019, 39(2): 294-302.

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